[Bioc-devel] not all bioc packages visible on github?

Mike Smith grimbough at gmail.com
Thu Jan 25 09:13:04 CET 2018

git.bioconductor.org is the canonical source for all Bioconductor
packages.  Every Bioconductor package can be cloned from there, with a
master branch representing Bioc-devel and separate named branches for all
previous releases.  However, it has no real visual interface, and I treat
it in a similar way to the old SVN repository, pushing changes when needed
but otherwise interacting with it very little.

Given this, many package developers choose to maintain a public version
somewhere else as well.  For example, I maintain the a rhdf5 package via a
Github repository at https://github.com/grimbough/rhdf5 and consider this
like a 'super-devel' branch.  Not every push made there will be matched by
a push to git.bioconductor.org but once I'm happy I've left it in a working
state I will sync the master branches on both repos. It also provides
access to all the nice social coding facilities of Github like issues, pull
requests, code searching, etc that aren't really available via

https://github.com/Bioconductor fulfills a similar role for the BioC core
team.  It is the public facing account for packages that the core team
maintain, rather than the project as a whole.  Maybe it would have been
better named 'BioC-Core' or some such to avoid this confusion, but it is
what it is.

It looks like you're the maintainer for BrowserViz, so it's up to you how
you proceed.  You can either clone it from git.bioconductor.org exactly as
you have done, create a new branch, make changes, and merge them back all
locally on your machine.  Then push the modified master branch back to
git.bioconductor.org when you're done.  Alternatively, you can choose to
make your own Github repo and follow that paradigm, in which case there are
some nice instructions at


On 25 January 2018 at 03:12, Robert M. Flight <rflight79 at gmail.com> wrote:

> Paul,
> My understanding was that the Bioconductor github repos were going to die,
> and it was up to the maintainer where the source was, and a public source
> need not be available. I asked about this previously, and there was too
> much confusion between the official Bioconductor repos and developers
> personal repos, I believe (Nitesh or others please correct me if I've
> gotten the details wrong).
> Hope that helps,
> -Robert
> On Wed, Jan 24, 2018 at 8:27 PM Paul Shannon <
> paul.thurmond.shannon at gmail.com> wrote:
> > By example:
> >
> > https://github.com/Bioconductor/KEGGREST    -> github project homepage
> > displays
> > https://github.com/Bioconductor/BrowserViz  -> 404
> >
> > Yet this works fine:
> >
> >   git clone git at git.bioconductor.org:packages/BrowserViz.git
> >
> > Is visibility at github.com/Bioconductor therefore conditional?
> >
> > My overall goal is to fork the BrowserViz repo, create a v2.0.0 branch,
> > merge back into devel after extensive refactoring.
> >
> > Advice welcome!
> >
> > Thank you.
> >
> >  - Paul
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
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